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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ), 'gf_id' => 'HOM05D001173', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001173' ), 'data_identifier' => 'HOM05D001173', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001173', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '529', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p16250' => 'bna', 'A04p17790' => 'bna', 'A07p02470' => 'bna', 'A08p23730' => 'bna', 'A09p58100' => 'bna', 'Aa31LG6G14110' => 'aar', 'Aa31LG6G16030' => 'aar', 'Aa31LG7G13670' => 'aar', 'Aa31LG7G14880' => 'aar', 'Aa31sc61G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1406' => 'aag', 'Actinidia00535' => 'ach', 'Actinidia01082' => 'ach', 'Actinidia03807' => 'ach', 'Actinidia16463' => 'ach', 'Actinidia17810' => 'ach', 'Actinidia27888' => 'ach', 'Actinidia36572' => 'ach', 'Actinidia38077' => 'ach', 'Ah.01g019250' => 'amhyb', 'Ah.03g141040' => 'amhyb', 'Ah.03g145890' => 'amhyb', 'Ah.03g145910' => 'amhyb', 'AL3G51500' => 'aly', 'AL3G52470' => 'aly', 'AL4G10800' => 'aly', 'AL4G13200' => 'aly', 'AL7G11190' => 'aly', 'Aqoxy5G01165' => 'aox', 'Aqoxy5G01591' => 'aox', 'Aqoxy6G01149' => 'aox', 'arahy.Tifrunner.gnm1.ann1.08WRUD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63Z2XK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8VTF5M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAS7TG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RPKW6C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U9XIEM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UT84T0' => 'arhy', 'AT2G18240' => 'ath', 'AT2G21600' => 'ath', 'AT2G23310' => 'ath', 'AT4G39220' => 'ath', 'ATR0568G116' => 'atr', 'ATR0724G048' => 'atr', 'Atru.chr13.444' => 'acertr', 'Atru.chr3.261' => 'acertr', 'Atru.chr5.3045' => 'acertr', 'AUR62003928' => 'cqu', 'AUR62004077' => 'cqu', 'AUR62011301' => 'cqu', 'AUR62016756' => 'cqu', 'AUR62016757' => 'cqu', 'AUR62038243' => 'cqu', 'BcaB03g12253' => 'bca', 'BcaB03g16613' => 'bca', 'BcaB06g27776' => 'bca', 'BcaB06g27889' => 'bca', 'BcaB08g34986' => 'bca', 'BcaC02g08556' => 'bca', 'BcaC02g08779' => 'bca', 'BcaC06g35215' => 'bca', 'BcaC06g36204' => 'bca', 'BcaC06g36389' => 'bca', 'BcaC07g41134' => 'bca', 'BcaNung02348' => 'bca', 'BcaNung03883' => 'bca', 'BolC3t20028H' => 'bol', 'BolC4t26671H' => 'bol', 'BolC7t40864H' => 'bol', 'BolC7t41072H' => 'bol', 'BolC7t42369H' => 'bol', 'BolC7t46740H' => 'bol', 'BolC8t51699H' => 'bol', 'BolC8t51911H' => 'bol', 'BraA04t17264Z' => 'bra', 'BraA04t17399Z' => 'bra', 'BraA07t28043Z' => 'bra', 'BraA08t34325Z' => 'bra', 'BraA09t41198Z' => 'bra', 'C03p77710' => 'bna', 'C04p50750' => 'bna', 'C04p52620' => 'bna', 'C07p04620' => 'bna', 'C07p06510' => 'bna', 'C07p18580' => 'bna', 'C07p63290' => 'bna', 'C08p41370' => 'bna', 'C08p43650' => 'bna', 'CAN.G1058.6' => 'can', 'CAN.G1812.5' => 'can', 'CAN.G222.149' => 'can', 'CAN.G222.164' => 'can', 'CANSAT25G0082' => 'cansat', 'CANSAT25G0891' => 'cansat', 'CANSAT25G0937' => 'cansat', 'CANSAT25G3112' => 'cansat', 'CANSAT25G3400' => 'cansat', 'CARHR108770' => 'chi', 'CARHR112550' => 'chi', 'CARHR247480' => 'chi', 'CARHR292950' => 'chi', 'Carub.0001s4236' => 'cru', 'Carub.0003s3007' => 'cru', 'Carub.0003s3241' => 'cru', 'Carub.0004s0252' => 'cru', 'Carub.0007s0113' => 'cru', 'Ca_20888_v3' => 'car', 'Ca_22127_v3' => 'car', 'Ca_24743_v3' => 'car', 'CBR_g23665' => 'cbr', 'Cc02_g17360' => 'ccan', 'Cc10_g04840' => 'ccan', 'CDE01G0683' => 'cde', 'CDE02G2032' => 'cde', 'CDE02G3363' => 'cde', 'CDE05G0601' => 'cde', 'CDE06G1206' => 'cde', 'CDE11G0323' => 'cde', 'Cfa004335' => 'cfa', 'Cfa018178' => 'cfa', 'Ciclev10002562m.g' => 'ccl', 'Ciclev10026506m.g' => 'ccl', 'Ciclev10026555m.g' => 'ccl', 'Ciclev10029324m.g' => 'ccl', 'CiPaw.01G013800' => 'cil', 'CiPaw.02G019600' => 'cil', 'CiPaw.05G066500' => 'cil', 'CiPaw.06G134400' => 'cil', 'ClCG01G017020' => 'cla', 'ClCG08G014980' => 'cla', 'ClCG11G004290' => 'cla', 'COL.COLO4_11473' => 'col', 'COL.COLO4_22047' => 'col', 'COL.COLO4_25957' => 'col', 'COL.COLO4_26283' => 'col', 'Cpa.g.sc123.49' => 'cpa', 'Cpa.g.sc55.100' => 'cpa', 'Cpa.g.sc62.170' => 'cpa', 'Cre12.g555350' => 'cre', 'CsaV3_2G014850' => 'csa', 'CsaV3_2G028800' => 'csa', 'CSS0015762' => 'camsi', 'CSS0018223' => 'camsi', 'CSS0020779' => 'camsi', 'CSS0030852' => 'camsi', 'CSS0035389' => 'camsi', 'CSS0042468' => 'camsi', 'DCAR_003665' => 'dca', 'DCAR_012793' => 'dca', 'DCAR_022477' => 'dca', 'DCAR_022983' => 'dca', 'Dinv23504' => 'din', 'Dinv26856' => 'din', 'Dinv30029' => 'din', 'Dinv35928' => 'din', 'Dinv36102' => 'din', 'Dinv39272' => 'din', 'Dinv40002' => 'din', 'Dinv42052' => 'din', 'Duzib041G0722' => 'dzi', 'Duzib052G0072' => 'dzi', 'Duzib132G0843' => 'dzi', 'Duzib147G1338' => 'dzi', 'Duzib248G1196' => 'dzi', 'Duzib248G1257' => 'dzi', 'Duzib264G1079' => 'dzi', 'ECA232G0364' => 'eca', 'ECA232G3493' => 'eca', 'ECA232G4771' => 'eca', 'ECA236G1818' => 'eca', 'ECA238G1601' => 'eca', 'ECA240G1166' => 'eca', 'EL10Ac6g15536' => 'bvu', 'EL10Ac6g15700' => 'bvu', 'EL10Ac9g21707' => 'bvu', 'Eucgr.F01585' => 'egr', 'Eucgr.G01613' => 'egr', 'Eucgr.G01688' => 'egr', 'Eucgr.I00805' => 'egr', 'Eucgr.I00807' => 'egr', 'Eucgr.I00863' => 'egr', 'FAN15G0587' => 'fan', 'FAN15G2909' => 'fan', 'FAN19G0056' => 'fan', 'FAN19G1172' => 'fan', 'FAN20G0683' => 'fan', 'FAN20G0805' => 'fan', 'FAN23G0136' => 'fan', 'FAN23G2452' => 'fan', 'FAN24G2050' => 'fan', 'FAN26G1864' => 'fan', 'FAN26G2445' => 'fan', 'FAN27G1243' => 'fan', 'FAN27G1961' => 'fan', 'FAN28G0756' => 'fan', 'FAN28G0918' => 'fan', 'FvH4_1g12980' => 'fve', 'FvH4_1g16570' => 'fve', 'FvH4_2g09170' => 'fve', 'FvH4_2g39600' => 'fve', 'Glyma.01G189400' => 'gma', 'Glyma.04G012100' => 'gma', 'Glyma.04G012200' => 'gma', 'Glyma.05G096900' => 'gma', 'Glyma.06G011900' => 'gma', 'Glyma.06G012000' => 'gma', 'Glyma.11G052801' => 'gma', 'Glyma.17G168200' => 'gma', 'Gohir.A01G004500' => 'ghi', 'Gohir.A02G155400' => 'ghi', 'Gohir.A02G166700' => 'ghi', 'Gohir.A03G195600' => 'ghi', 'Gohir.A06G009100' => 'ghi', 'Gohir.A11G196600' => 'ghi', 'Gohir.A12G029700' => 'ghi', 'Gohir.A13G033600' => 'ghi', 'Gohir.D01G004450' => 'ghi', 'Gohir.D02G216600' => 'ghi', 'Gohir.D02G216700' => 'ghi', 'Gohir.D03G013300' => 'ghi', 'Gohir.D03G025300' => 'ghi', 'Gohir.D06G004600' => 'ghi', 'Gohir.D11G202500' => 'ghi', 'Gohir.D12G029000' => 'ghi', 'Gohir.D13G031500' => 'ghi', 'Gorai.002G005400' => 'gra', 'Gorai.003G013600' => 'gra', 'Gorai.003G026900' => 'gra', 'Gorai.005G244700' => 'gra', 'Gorai.007G217100' => 'gra', 'Gorai.008G029700' => 'gra', 'Gorai.010G009200' => 'gra', 'Gorai.013G035900' => 'gra', 'GSVIVG01009734001' => 'vvi', 'GSVIVG01018931001' => 'vvi', 'GSVIVG01022061001' => 'vvi', 'GSVIVG01023802001' => 'vvi', 'HanXRQChr01g0030401' => 'han', 'HanXRQChr03g0067621' => 'han', 'HanXRQChr03g0074631' => 'han', 'HanXRQChr05g0135731' => 'han', 'HanXRQChr09g0269021' => 'han', 'HanXRQChr15g0479641' => 'han', 'HanXRQChr15g0481111' => 'han', 'HanXRQChr16g0501541' => 'han', 'Haze_02405' => 'cav', 'Haze_15067' => 'cav', 'Haze_15358' => 'cav', 'Haze_17939' => 'cav', 'Haze_26672' => 'cav', 'Haze_27461' => 'cav', 'Hma1.2p1_0066F.1_g036260' => 'hma', 'Hma1.2p1_0224F.1_g094530' => 'hma', 'Hma1.2p1_0360F.1_g135890' => 'hma', 'Hma1.2p1_0469F.1_g159030' => 'hma', 'Hma1.2p1_0634F.1_g193020' => 'hma', 'Hma1.2p1_0634F.1_g193025' => 'hma', 'Hma1.2p1_0789F.1_g218180' => 'hma', 'Hma1.2p1_2192F.1_g316720' => 'hma', 'Hma1.2p1_2192F.1_g316729' => 'hma', 'Hma1.2p1_2192F.1_g316743' => 'hma', 'Hma1.2p1_2496F.1_g323310' => 'hma', 'Hma1.2p1_2496F.1_g323315' => 'hma', 'Hma1.2p1_2496F.1_g323322' => 'hma', 'Hma1.2p1_2496F.1_g323324' => 'hma', 'Hma1.2p1_2648F.1_g326120' => 'hma', 'HPP92_004778' => 'vpl', 'HPP92_021333' => 'vpl', 'HPP92_021821' => 'vpl', 'HPP92_023421' => 'vpl', 'Hund00250' => 'sun', 'Hund06243' => 'sun', 'Hund13909' => 'sun', 'Hund13991' => 'sun', 'Hund16363' => 'sun', 'Hund16441' => 'sun', 'Lalb_Chr01g0002471' => 'lal', 'Lalb_Chr05g0226291' => 'lal', 'Lalb_Chr09g0323361' => 'lal', 'Lalb_Chr09g0333871' => 'lal', 'Lalb_Chr16g0388791' => 'lal', 'Lalb_Chr19g0138671' => 'lal', 'Lj1g0012514' => 'lja', 'Lj2g0028157' => 'lja', 'Lj3g0014972' => 'lja', 'Lj4A63G82' => 'lonja', 'Lj4A766G65' => 'lonja', 'Lj4C788G10' => 'lonja', 'Lj4g0011723' => 'lja', 'Lj7C75T6' => 'lonja', 'Lj7C82G4' => 'lonja', 'Lj9A374T111' => 'lonja', 'Lsat_1_v5_gn_1_22441' => 'lsa', 'Lsat_1_v5_gn_2_85620' => 'lsa', 'Lsat_1_v5_gn_4_117761' => 'lsa', 'Lsat_1_v5_gn_4_127661' => 'lsa', 'Lsat_1_v5_gn_5_177881' => 'lsa', 'Lsat_1_v5_gn_7_91001' => 'lsa', 'Lsat_1_v5_gn_9_108881' => 'lsa', 'Manes.01G137100' => 'mes', 'Manes.02G095800' => 'mes', 'Manes.04G089400' => 'mes', 'Manes.05G157700' => 'mes', 'Manes.11G085700' => 'mes', 'Manes.12G107900' => 'mes', 'Manes.13G119300' => 'mes', 'Manes.18G022800' => 'mes', 'Mapoly0028s0076' => 'mpo', 'MBI10_g18273_MAGBIO' => 'mbi', 'MBI17_g41605_MAGBIO' => 'mbi', 'MCO12G021' => 'mco', 'MD02G1144300' => 'mdo', 'MD08G1029200' => 'mdo', 'MD12G1092000' => 'mdo', 'MD15G1024700' => 'mdo', 'MD15G1257900' => 'mdo', 'MD15G1258000' => 'mdo', 'MD15G1287700' => 'mdo', 'Medtr4g070400' => 'mtr', 'Medtr4g094930' => 'mtr', 'Medtr5g016560' => 'mtr', 'MELO3C010950.2' => 'cme', 'MELO3C023307.2' => 'cme', 'Migut.B00224' => 'egut', 'Migut.H00403' => 'egut', 'Migut.J00607' => 'egut', 'Migut.L00180' => 'egut', 'Migut.N01248' => 'egut', 'Migut.N02729' => 'egut', 'MSTRG.15372' => 'ama', 'MSTRG.16817' => 'ama', 'MSTRG.22247' => 'ama', 'MSTRG.25185' => 'ama', 'MSTRG.27692' => 'ama', 'MSTRG.5401' => 'ama', 'Nitab4.5_0000017g0220' => 'nta', 'Nitab4.5_0000029g0020' => 'nta', 'Nitab4.5_0000308g0290' => 'nta', 'Nitab4.5_0001039g0050' => 'nta', 'Nitab4.5_0001052g0060' => 'nta', 'Nitab4.5_0001052g0070' => 'nta', 'Nitab4.5_0001373g0080' => 'nta', 'Nitab4.5_0001391g0010' => 'nta', 'Nitab4.5_0003539g0020' => 'nta', 'Nitab4.5_0003727g0030' => 'nta', 'Nitab4.5_0004339g0070' => 'nta', 'Nitab4.5_0004531g0030' => 'nta', 'Nitab4.5_0004757g0030' => 'nta', 'Nitab4.5_0006352g0010' => 'nta', 'Nitab4.5_0009972g0020' => 'nta', 'Nitab4.5_0010118g0040' => 'nta', 'Nn1g02855' => 'nnu', 'Nn1g04737' => 'nnu', 'Nn1g04937' => 'nnu', 'Nn5g29650' => 'nnu', 'Nn5g30390' => 'nnu', 'Oeu003724.1' => 'oeu', 'Oeu013241.1' => 'oeu', 'Oeu014789.1' => 'oeu', 'Oeu026184.1' => 'oeu', 'Oeu029824.1' => 'oeu', 'Oeu036204.1' => 'oeu', 'Oeu041634.1' => 'oeu', 'Oeu045703.1' => 'oeu', 'Oeu054786.1' => 'oeu', 'Oeu055596.1' => 'oeu', 'Oeu061214.1' => 'oeu', 'Os01g0106200' => 'osa', 'Os06g0708300' => 'osa', 'Os08g0309300' => 'osa', 'Os12g0439700' => 'osa', 'Peaxi162Scf00003g01220' => 'pax', 'Peaxi162Scf00016g00621' => 'pax', 'Peaxi162Scf00303g00513' => 'pax', 'Peaxi162Scf00549g00315' => 'pax', 'Peaxi162Scf01087g00127' => 'pax', 'PGR004G2559' => 'pgr', 'PGR031G0422' => 'pgr', 'PGR042G3362' => 'pgr', 'PGSC0003DMG400000734' => 'stu', 'PGSC0003DMG400007945' => 'stu', 'PGSC0003DMG400024959' => 'stu', 'Phvul.002G015800' => 'pvu', 'Phvul.003G240700' => 'pvu', 'Phvul.009G023300' => 'pvu', 'Phvul.011G044200' => 'pvu', 'Potri.002G034200' => 'ptr', 'Potri.004G156800' => 'ptr', 'Potri.004G156900' => 'ptr', 'Potri.005G141700' => 'ptr', 'Potri.005G228900' => 'ptr', 'Potri.007G047800' => 'ptr', 'Potri.009G118500' => 'ptr', 'Pp3c18_21970' => 'ppa', 'Pp3c19_21230' => 'ppa', 'Pp3c22_2310' => 'ppa', 'PRCOL_00001247' => 'pco', 'Prupe.1G377000' => 'ppe', 'Prupe.6G230200' => 'ppe', 'Prupe.7G157300' => 'ppe', 'Prupe.8G094300' => 'ppe', 'Psat0s3539g0080' => 'psa', 'Psat0s859g0040' => 'psa', 'Psat2g168080' => 'psa', 'PSO170G1780' => 'pso', 'PSO170G3508' => 'pso', 'PSO210G2875' => 'pso', 'PSO541G2728' => 'pso', 'PSO675G7041' => 'pso', 'PSO764G0013' => 'pso', 'QL02p009082' => 'qlo', 'QL06p046956' => 'qlo', 'QL08p020541' => 'qlo', 'QL11p044494' => 'qlo', 'RcHm_v2.0_Chr1g0343311' => 'rch', 'RcHm_v2.0_Chr2g0101041' => 'rch', 'RcHm_v2.0_Chr2g0101051' => 'rch', 'RcHm_v2.0_Chr2g0106471' => 'rch', 'RcHm_v2.0_Chr2g0106481' => 'rch', 'RcHm_v2.0_Chr4g0389971' => 'rch', 'RcHm_v2.0_Chr4g0411361' => 'rch', 'RcHm_v2.0_Chr6g0247461' => 'rch', 'RcHm_v2.0_Chr6g0301161' => 'rch', 'RcHm_v2.0_Chr6g0301321' => 'rch', 'RcHm_v2.0_Chr7g0237871' => 'rch', 'Rhsim05G0073500' => 'rsi', 'Rhsim08G0098000' => 'rsi', 'Rhsim11G0178900' => 'rsi', 'Sabra02G0027500' => 'sbr', 'Sabra04G0104700' => 'sbr', 'Sabra04G0104800' => 'sbr', 'Sabra05G0113200' => 'sbr', 'Sabra05G0176800' => 'sbr', 'Sabra07G0042800' => 'sbr', 'Sabra09G0090800' => 'sbr', 'SalBow5G0301' => 'sbo', 'SalBow5G5257' => 'sbo', 'SalBow6G1928' => 'sbo', 'SalBow6G1981' => 'sbo', 'SalBow6G3829' => 'sbo', 'SalBow6G4462' => 'sbo', 'SalBow6G5287' => 'sbo', 'Sc07g0000670' => 'sci', 'Sc08g0000590' => 'sci', 'Sc16g0002640' => 'sci', 'Sc16g0005660' => 'sci', 'Sc26g0003540' => 'sci', 'Sed0002211' => 'sed', 'Sed0002809' => 'sed', 'Sed0012921' => 'sed', 'Sed0013786' => 'sed', 'Sed0015667' => 'sed', 'Sed0024567' => 'sed', 'SEGI_02771' => 'sgi', 'SEGI_08149' => 'sgi', 'SEGI_10335' => 'sgi', 'SGA_v2.0_scaffold124G33584' => 'sas', 'SGA_v2.0_scaffold125G33728' => 'sas', 'SGA_v2.0_scaffold14G06986' => 'sas', 'SGA_v2.0_scaffold15G07358' => 'sas', 'SGA_v2.0_scaffold201G41403' => 'sas', 'SGA_v2.0_scaffold28G11798' => 'sas', 'SMO114G0108' => 'smo', 'SMO361G0129' => 'smo', 'Solyc01g109770.3' => 'sly', 'Solyc02g093010.3' => 'sly', 'Sopen01g051960' => 'spe', 'Sopen02g037570' => 'spe', 'Sopen04g032110' => 'spe', 'Sp3g31650' => 'spa', 'Sp4g00760' => 'spa', 'Sp4g02310' => 'spa', 'Sp7g34900' => 'spa', 'Sp7g36620' => 'spa', 'TAR376G1192' => 'tar', 'TAR376G1216' => 'tar', 'TAR381G0520' => 'tar', 'TAR381G1291' => 'tar', 'TAR381G1501' => 'tar', 'TAR625G0018' => 'tar', 'TAR628G0007' => 'tar', 'TAR628G0273' => 'tar', 'TAR628G1431' => 'tar', 'THA.LOC104804127' => 'tha', 'THA.LOC104804352' => 'tha', 'THA.LOC104807311' => 'tha', 'THA.LOC104807462' => 'tha', 'THA.LOC104807599' => 'tha', 'THA.LOC104807740' => 'tha', 'THA.LOC104819777' => 'tha', 'THA.LOC104819858' => 'tha', 'THA.LOC104824818' => 'tha', 'Thecc.01G032300' => 'tca', 'Thecc.01G062400' => 'tca', 'Thecc.02G082900' => 'tca', 'Thecc.08G029800' => 'tca', 'Thhalv10000326m.g' => 'esa', 'Thhalv10000333m.g' => 'esa', 'Thhalv10022825m.g' => 'esa', 'Thhalv10022852m.g' => 'esa', 'Thhalv10026272m.g' => 'esa', 'Thhalv10026317m.g' => 'esa', 'TPR.G14584' => 'tpr', 'TPR.G22542' => 'tpr', 'TPR.G26903' => 'tpr', 'TWI09G0233' => 'twi', 'TWI09G0864' => 'twi', 'TWI31G0482' => 'twi', 'TWI53G1365' => 'twi', 'TWI73G0066' => 'twi', 'TWI73G0685' => 'twi', 'TWI79G1674' => 'twi', 'unitig_22.g5171' => 'ugi', 'unitig_26.g10249' => 'ugi', 'unitig_8.g3370' => 'ugi', 'unitig_8.g4047' => 'ugi', 'unitig_9.g29491' => 'ugi', 'vmacro02091' => 'vma', 'vmacro04561' => 'vma', 'vmacro17481' => 'vma', 'vmacro17972' => 'vma', 'VMungo0251G1571' => 'vmu', 'VMungo1127G1948' => 'vmu', 'VMungo1215G0988' => 'vmu', 'VMungo1309G2355' => 'vmu', 'Zm00001eb126790' => 'zma', 'Zm00001eb227430' => 'zma', 'Zm00001eb334220' => 'zma', 'Zm00001eb383410' => 'zma' ) $gf_id = 'HOM05D001173' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001173' ) $data_identifier = 'HOM05D001173' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 6, 'hma' => (int) 15, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 7, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 16, 'nnu' => (int) 5, 'oeu' => (int) 11, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 11, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 9, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb383410' $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